3B7W
Crystal structure of human acyl-CoA synthetase medium-chain family member 2A, with L64P mutation
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1PG3 | PDB entry 1PG3 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 0.1M HEPES pH 7.5, 1.4M Na citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.75 | 67.22 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 98.426 | α = 90 |
b = 109.173 | β = 90 |
c = 176.926 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 2 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS HTC | OSMIC MIRRORS | 2007-09-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
1 | 2 | 50.57 | 98.9 | 0.077 | 0.04 | 12.8 | 4.6 | 63810 | 60580 | 2.06 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2 | 2.11 | 98.2 | 0.872 | 0.446 | 2 | 4.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1PG3 | 2 | 50 | 60580 | 60580 | 3225 | 98.81 | 0.17136 | 0.16903 | 0.21385 | RANDOM | 28.86 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.85 | 0.8 | 1.05 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.624 |
r_dihedral_angle_4_deg | 16.409 |
r_dihedral_angle_3_deg | 13.089 |
r_scangle_it | 9.204 |
r_scbond_it | 7.72 |
r_dihedral_angle_1_deg | 6.089 |
r_mcangle_it | 4.599 |
r_mcbond_it | 3.823 |
r_angle_refined_deg | 1.446 |
r_mcbond_other | 1.159 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4126 |
Nucleic Acid Atoms | |
Solvent Atoms | 458 |
Heterogen Atoms | 11 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |